Abstract
Plasma and serum are rich sources of proteins that are commonly used for clinical proteome profiling and biomarkers discovery. However, high-throughput plasma proteome profiling and quantitative analysis using mass spectrometry are challenging because of the large dynamic range of protein abundance and complexity. To overcome these challenges, we developed a convenient high-throughput workflow of depleted plasma using the 4D-Proteomics feature of the Bruker timsTOF Pro mass spectrometer with data-dependent (PASEF) and data-independent acquisition (diaPASEF) method that can potentially be used in a clinical proteome profiling and biomarker discoveries. This workflow is robust, optimal for high throughput, high proteome depth, and is reproducible. In our sample preparation steps, we used immuno-depletion steps to remove high-abundance plasma proteins, and without any further cleanup steps, we can use depleted plasma samples directly for enzymatic digestion. Immuno-depletion steps and 4D-Proteomics features of timsTOF Pro increase the plasma proteome depth, and accuracy with the identification of >800 protein groups.
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Acknowledgments
We thank 2P30 CA013696-45 Cancer Center Support Grant for providing support for this project.
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Soni, R.K. (2022). High-Throughput Plasma Proteomic Profiling. In: Garg, U. (eds) Clinical Applications of Mass Spectrometry in Biomolecular Analysis. Methods in Molecular Biology, vol 2546. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2565-1_36
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DOI: https://doi.org/10.1007/978-1-0716-2565-1_36
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